Transition to taxon Transition to taxon concepts from a world of concepts from a world of

legacy datalegacy data--- --- R.K. PeetR.K. Peet11, A.S. Weakley, A.S. Weakley1,21,2, ,

X. LiuX. Liu1,31,3, & N. Franz, & N. Franz4,54,5

1The University of North Carolina at Chapel Hill2The North Carolina Botanical Garden

3National Evolutionary Synthesis Center4National Center for Ecological Anal. & Synthesis

5University of Puerto Rico, Mayagüez

Taxonomic database Taxonomic database challengechallenge

The well-known problem:The well-known problem:Integration of data from different Integration of data from different times & places, by multiple times & places, by multiple investigators using varied taxonomic investigators using varied taxonomic standards.standards.

The well-known solution:The well-known solution: Identifications to taxon concepts that Identifications to taxon concepts that have mapped relationships to related have mapped relationships to related concepts.concepts.

The good news:The good news: • TDWG has embraced taxonomic TDWG has embraced taxonomic concepts and adopted TCS. concepts and adopted TCS.

• Multiple organizations are developing Multiple organizations are developing tools for concept use and integration. tools for concept use and integration.

The challenge:The challenge:• Few large-scale compilations of Few large-scale compilations of concepts and their relationships are concepts and their relationships are available.available.

• Legacy data lacking concept Legacy data lacking concept annotation will be around forever.annotation will be around forever.

A Case Study:A Case Study:Flora of the Southeastern Flora of the Southeastern

USUS

1.1. Regional floras were badly obsolete and Regional floras were badly obsolete and incompleteincomplete

2.2. No flora covered the Atlantic SENo flora covered the Atlantic SE

3.3. Ecological datasets with multiple Ecological datasets with multiple taxonomic authorities and inconsistent taxonomic authorities and inconsistent taxonomic concepts defied integrationtaxonomic concepts defied integration

4.4. Need for an updated atlas of the flora of Need for an updated atlas of the flora of the Southeastthe Southeast

5.5. Good candidate for a demonstrationGood candidate for a demonstration

Critical SE floristic works Critical SE floristic works

1.1. Weakley 2005. Flora of the Carolinas, Virginia, Georgia, and Weakley 2005. Flora of the Carolinas, Virginia, Georgia, and Surrounding AreasSurrounding Areas

2.2. Small 1933. Manual of the southeastern flora Small 1933. Manual of the southeastern flora 3.3. Fernald 1950. Gray's manual of botanyFernald 1950. Gray's manual of botany4.4. Gleason 1952. Britton and Brown illustrated flora Gleason 1952. Britton and Brown illustrated flora 5.5. Radford, Ahles & Bell 1968. Manual of the vascular flora of the Radford, Ahles & Bell 1968. Manual of the vascular flora of the

CarolinasCarolinas6.6. Gleason & Cronquist 1991. Manual of vascular plants of Gleason & Cronquist 1991. Manual of vascular plants of

northeastern United States and adjacent Canadanortheastern United States and adjacent Canada7.7. 1993-2005. Flora of North America north of Mexico1993-2005. Flora of North America north of Mexico8.8. Kartesz 1999. A synonymized checklist for the vascular flora of Kartesz 1999. A synonymized checklist for the vascular flora of

the United States, Canada, and Greenlandthe United States, Canada, and Greenland9.9. Wofford 1989. Vascular Plants of the Blue Ridge Wofford 1989. Vascular Plants of the Blue Ridge 10.10.Godfrey & Wooton 1979. Aquatic and Wetland Plants of Godfrey & Wooton 1979. Aquatic and Wetland Plants of

Southeastern United StatesSoutheastern United States11.11.1980-1990. Vascular Flora of the Southeastern United States1980-1990. Vascular Flora of the Southeastern United States12.12. Recent monographs and revisions (>2000)Recent monographs and revisions (>2000)

Andropogon virginicusAndropogon virginicus complex in the complex in the CarolinasCarolinas

9 elemental units; 17 base concepts, 27 scientific names9 elemental units; 17 base concepts, 27 scientific names

Massive ImportMassive Import

• Scanned indices -- OCRScanned indices -- OCR

• Spreadsheets for preliminary concept Spreadsheets for preliminary concept documentationdocumentation

• Import into software tool for Import into software tool for managing concepts and relationshipsmanaging concepts and relationships

ConceptMapperConceptMapper • Document and manage taxon Document and manage taxon

concepts from multiple sourcesconcepts from multiple sources

• Document and manage concept Document and manage concept relationships from multiple sourcesrelationships from multiple sources

• Input data files as txt, xls, mdb, or Input data files as txt, xls, mdb, or TCS-XMLTCS-XML

• Export data as txt, mdb, or TCS-XMLExport data as txt, mdb, or TCS-XML

http://152.2.14.231/conceptmapper/

Concept mapper

How have things changed?How have things changed?Concept relationships of Southeastern US Concept relationships of Southeastern US

plants treated in different floras.plants treated in different floras.

Based on > 50,000 concept Based on > 50,000 concept relationshipsrelationships

http://http://herbarium.unc.edu/flora.htmherbarium.unc.edu/flora.htm

Toward a new AtlasToward a new Atlas

Carya carolinae-septentrionalisCarya carolinae-septentrionalis, Radford et al. 1968, Radford et al. 1968

How to How to integrate integrate new new sources of sources of data??data??

http://herbarium.unc.edu/seflora/firstviewer.htm

Add dynamic access to NCU Add dynamic access to NCU collectioncollection

Carya carolinae-septentrionalisCarya carolinae-septentrionalis

NCUNCU

RABRAB

Carya carolinae-septentrionalisCarya carolinae-septentrionalis

NCUNCU

RABRAB

USDAUSDA

CVSCVS

Add USDA PLANTS records & Add USDA PLANTS records & CVS vegetation plot dataCVS vegetation plot data

But wait !!But wait !!There is a concept issueThere is a concept issue

• According to Radford 1968, USDA According to Radford 1968, USDA PLANTS v 4.0, & Weakley 2005PLANTS v 4.0, & Weakley 2005– Carya carolinae-septentrionalisCarya carolinae-septentrionalis– Carya ovataCarya ovata

• According to Stone 1997 in FNAAccording to Stone 1997 in FNA– Carya ovata var australisCarya ovata var australis– Carya ovata var. ovataCarya ovata var. ovata

How to merge records that may be based on different concepts??• Weakley 2005 – Reference conceptsWeakley 2005 – Reference concepts• Radford 1968 – Concepts mappedRadford 1968 – Concepts mapped• NC Heritage Program – Weakley conceptsNC Heritage Program – Weakley concepts• CVS – Weakley concepts (mostly)CVS – Weakley concepts (mostly)• USDA – Kartesz 1999 concepts (mostly)USDA – Kartesz 1999 concepts (mostly)• NCU & NCSC – Nominal concepts onlyNCU & NCSC – Nominal concepts only

Most museum collection identifications Most museum collection identifications must be interpreted as nominal must be interpreted as nominal concepts!! To do otherwise would be to concepts!! To do otherwise would be to introduce false positives.introduce false positives.

Carya carolinae-septentrionalisCarya carolinae-septentrionalis

Nominal occurrences represent occurrences Nominal occurrences represent occurrences that might that might or might notor might not represent the taxon represent the taxon

All specimens of All specimens of Carya ovataCarya ovata must must be identified to nominal conceptsbe identified to nominal concepts

Consider Consider CleistesCleistes• Cleistes bifariaCleistes bifaria was split off was split off C. divaricataC. divaricata

after Radford et al. was published. after Radford et al. was published.

• Radford et al. records must be mapped Radford et al. records must be mapped as ambiguous.as ambiguous.

• Kartesz incorrectly maps all Kartesz incorrectly maps all CleistesCleistes in the Carolinas as in the Carolinas as C. divaricataC. divaricata owing to uncritical owing to uncritical import of records from Radford.import of records from Radford.

http://herbarium.unc.edu/seflora/firstviewer.htm

Other data are linked by name and conceptOther data are linked by name and concept

Specimens matching the name

• ..\..\New Folder\Snap32.jpg

Images matching the name

Community types with the concept

Link to Vegetation plots with the taxon

CategoCategoryry

ExplanationExplanation

OriginalOriginal Appears in the reference where the new name/typeAppears in the reference where the new name/typeassociation was established.association was established.Example:Example: Andropogon virginicusAndropogon virginicus L. sec. L. sec. Linnaeus Linnaeus

(1753).(1753).

RevisionalRevisional Appears in a comprehensive revision of an existingAppears in a comprehensive revision of an existingTaxonomic name and lineage, e.g. a monograph.Taxonomic name and lineage, e.g. a monograph.Example:Example: Andropogon virginicusAndropogon virginicus L. sec. Campbell L. sec. Campbell

(1983).(1983).

RelationalRelational Appears in a comprehensive compilation withoutAppears in a comprehensive compilation withoutdescriptions); meaning may be inferred from the list of descriptions); meaning may be inferred from the list of mutually exclusive concepts.mutually exclusive concepts.Example:Example: Andropogon virginicusAndropogon virginicus L. sec. ITIS (2006). L. sec. ITIS (2006).

InformalInformal Appears in a taxonomic treatment yet is poorly Appears in a taxonomic treatment yet is poorly specified, specified,

being outside of the focal names and taxa.being outside of the focal names and taxa.Example:Example: Andropogon halliiAndropogon hallii Hackel sec. Weakley Hackel sec. Weakley

(2006).(2006).(“a Midwestern species”)(“a Midwestern species”)

NominalNominal Appears outside of the context of a particular source;Appears outside of the context of a particular source;indirectly links to all other concepts with the name.indirectly links to all other concepts with the name.Example:Example: Andropogon virginicusAndropogon virginicus L. L.

Types of Concepts

Objectives:Objectives:• Allow user to select date-specific Allow user to select date-specific

version of Weakley.version of Weakley.• Allow user to select a Weakley, Allow user to select a Weakley,

PLANTS, or FNA perspective.PLANTS, or FNA perspective.

Data needs:Data needs:• Map relationships to PLANTS v 4.0Map relationships to PLANTS v 4.0• Map relationships between PLANTS Map relationships between PLANTS

and FNAand FNA• Date-stamp changes in Weakley Date-stamp changes in Weakley

Next step?Next step?

Multiple party Multiple party perspectivesperspectives

LinksLinksConceptMapperConceptMapperhttp://152.2.14.231/conceptmapper/

Weakley floraWeakley florahttp://herbarium.unc.edu/flora.htm

NCU Atlas of the SE floraNCU Atlas of the SE florahttp://herbarium.unc.edu/seflora/firstviewer.htm

ThanksThanks NSF (SEEK, VegBank) & the NC Botanical Garden